PDBsum entry 1a3i

Extracellular matrix

PDB id: 1a3i

Contents

Ligands

PRO-PRO-GLY-PRO-PRO-GLY-PRO-PRO-GLY

PRO-PRO-GLY-PRO-PRO-GLY ×2

ACY ×2

Waters ×37

PDB id:

1a3i

Name:

Extracellular matrix

Title:

X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (pro-pro-gly)

Structure:

Collagen-like peptide. Chain: a. Engineered: yes. Collagen-like peptide. Chain: b, c. Engineered: yes

Source:

not given

Resolution:

1.97Å R-factor: 0.181

Authors:

R.Z.Kramer,L.Vitagliano,J.Bella,R.Berisio,L.Mazzarella,B.Brodsky, A.Zagari,H.M.Berman

Key ref:

R.Z.Kramer et al. (1998). X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly). J Mol Biol, 280, 623-638. PubMed id: 9677293 DOI: 10.1006/jmbi.1998.1881

Date:

22-Jan-98 Release date: 06-May-98

DOI no: 10.1006/jmbi.1998.1881

J Mol Biol 280:623-638 (1998)

PubMed id: 9677293

X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly).

R.Z.Kramer, L.Vitagliano, J.Bella, R.Berisio, L.Mazzarella, B.Brodsky, A.Zagari, H.M.Berman.

ABSTRACT

The crystal structure of the triple-helical peptide (Pro-Pro-Gly)10 has been re-determined to obtain a more accurate description for this widely studied collagen model and to provide a comparison with the recent high-resolution crystal structure of a collagen-like peptide containing Pro-Hyp-Gly regions. This structure demonstrated that hydroxyproline participates extensively in a repetitive hydrogen-bonded assembly between the peptide and the solvent molecules. Two separate structural studies of the peptide (Pro-Pro-Gly)10 were performed with different crystallization conditions, data collection temperatures, and X-ray sources. The polymer-like structure of one triple-helical repeat of Pro-Pro-Gly has been determined to 2.0 A resolution in one case and 1.7 A resolution in the other. The solvent structures of the two peptides were independently determined specifically for validation purposes. The two structures display a reverse chain trace compared with the original structure determination. In comparison with the Hyp-containing peptide, the two Pro-Pro-Gly structures demonstrate very similar molecular conformation and analogous hydration patterns involving carbonyl groups, but have different crystal packing. This difference in crystal packing indicates that the involvement of hydroxyproline in an extended hydration network is critical for the lateral assembly and supermolecular structure of collagen.

Selected figure(s)

Figure 5.
Figure 5. Examples of hydration structure in the (a) Gly!Ala structure (b) PPG 1 or PPG 2 and (c) PPG 0 struc- tures. In (a) and (b) two water molecules are bound to the carbonyl group of the Y position proline residue (WA and WN) and one water molecule is bound to the glycine carbonyl group (WN). In (a) two additional water molecules are bound to O d of the hydroxyproline residue. Inter- and intrachain water bridges are then formed by interconnecting water molecules. In general, the water structure of PPG shows repetitive pentagonal-like inter and intrachain bridges between carbonyl groups. In (c) two water molecules, W1 and W2, are bound to the carbonyl group of the Y position proline residue. W1 is also bound to the glycine carbonyl group, forming a one water molecule intrachain bridge. W1 and W2 are connected by W3, forming a three water molecule interchain bridge similar to that seen in (a) and (b). The Figure was generated with MOLSCRIPT (Kraulis, 1991).

Figure 9.
Figure 9. Comparing model A with model B from initial molecular replacement. (a) Model A. Presumably, the carbo- nyl group of the proline residue in the X position should make a hydrogen bonding contact with the N atom of the glycine residue in the neighboring chain. Model A displays ``normal'', N(Gly) to O(Pro)X hydrogen bonds in terms of length and orientation (broken single line). The distance to the C a of the third chain is longer and the orientation is not as appropriate for a hydrogen bond (broken double line). (b) Model B. Interchain hydrogen bonding geometry is per- turbed. In model B, the oxygen atom appears to be some- what pointed toward the C a (broken double line), rather than toward the N(Gly), and this length is reasonable for a hydrogen bond while the distance to the N(Gly) becomes longer (broken single line). (c) The high-symmetry sequence and quasi-infinite helical nature of Pro-Pro-Gly implies that an end-to-end rotation of the peptide chain would give ana- logous models with only the N and C a positions transposed. Parts (a) and (b) of the Figure were generated with MOL- SCRIPT (Kraulis, 1991).

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 280, 623-638) copyright 1998.

Figures were selected by an automated process.